Microbial ecologists seek understanding of the ways microorganisms interact with each other and with their environment. Much research in this area uses molecular techniques, either to probe the diversity of complex populations and communities, or to ask specific questions about gene expression and organismal function within natural environments.

Research topics include bioremediation, microbial mediated ecosystem functions, microbial evolution, population genetics and breeding biology of microbes, plant-microbe symbioses, and the structure and function of microbial communities.